PURPOSE: Molecular testing in non-small cell lung cancer (NSCLC) aids in identifying oncogenic alterations. The aim of this study was to compare the rates of detection of oncogenic alterations and responsiveness to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) according to EGFR mutation status as determined by peptide nucleic acid (PNA) clamping or direct sequencing (DS). MATERIALS AND METHODS: We performed a systematic literature search using MEDLINE, EMBASE, and the Cochrane Central Register. Data from included studies were pooled to yield summary sensitivity, specificity, positive and negative likelihood ratios, diagnostic odds ratio, and receiver operating characteristic curves. A meta-regression analysis was conducted to identify potential sources of heterogeneity between selected studies. RESULTS: We identified 10 studies comprising 924 patients. Oncogenic alterations were detected in 340 of 924 cases (36.8%) with PNA clamping and in 250 of 924 (27.1%) with DS. The pooled sensitivities of PNA clamping and DS were 0.93 [95% confidence interval (CI): 0.90−0.95] and 0.69 (95% CI: 0.64−0.73), respectively. According to meta-regression analysis, none of the covariates were found to be significant sources of heterogeneity. With respect to treatment responses to EGFR-TKIs, there was no significant difference therein between EGFR mutations detected by PNA clamping and DS (53.4% vs. 50.8%; risk ratio, 0.99; 95% CI 0.83−1.19; p=0.874). CONCLUSION: We demonstrated that PNA clamping has a higher sensitivity than DS for detecting oncogenic alterations in NSCLC. Our findings suggest that PNA clamping is a more useful method for clinical practice.
Antineoplastic Agents/therapeutic use ; Carcinoma, Non-Small-Cell Lung/drug therapy/*genetics ; Constriction ; Humans ; Lung Neoplasms/*genetics ; Molecular Diagnostic Techniques ; Mutation ; Peptide Nucleic Acids/*genetics ; Protein Kinase Inhibitors/*therapeutic use ; Receptor Protein-Tyrosine Kinases/*genetics ; Receptor, Epidermal Growth Factor/*genetics ; Sensitivity and Specificity ; Sequence Analysis ; Sequence Analysis, DNA ; Translocation, Genetic

The lipid droplet (LD) is a unique multi-functional organelle that contains a neutral lipid core covered with a phospholipid monolayer membrane. The LDs have been found in almost all organisms from bacteria to humans with similar shape. Several conserved functions of LDs have been revealed by recent studies, including lipid metabolism and trafficking, as well as nucleic acid binding and protection. We summarized these findings and proposed a hypothesis that the LD is a conserved organelle.
Animals ; Bacteria ; metabolism ; ultrastructure ; Biological Evolution ; Cholesterol Esters ; metabolism ; Humans ; Lipid Droplets ; chemistry ; metabolism ; ultrastructure ; Lipid Metabolism ; genetics ; Nucleic Acids ; metabolism ; Peptide Initiation Factors ; chemistry ; metabolism ; Protein Binding ; RNA-Binding Proteins ; chemistry ; metabolism ; Ribosome Subunits ; chemistry ; metabolism ; Triglycerides ; metabolism

PURPOSE: The BRAF(V600E) mutation represents a novel indicator of the progression and aggressiveness of papillary thyroid carcinoma (PTC). The purpose of this study was to determine the clinical significance of free circulating mutant BRAF(V600E) in predicting the advanced disease of PTC. MATERIALS AND METHODS: Seventy seven matched tumor and plasma samples obtained from patients with both benign and PTC were analyzed for BRAF(V600E) mutation using a peptide nucleic acid (PNA) clamp real-time polymerase chain reaction (PCR). RESULTS: The BRAF(V600E) mutation was absent in tumor DNA samples obtained from patients with benign follicular adenomas or adenomatous goiter. In contrast, 49 of 72 (68.1%) PTC tumors were positive for the BRAF(V600E) mutation. Among them, 3 (6.1%) patients with PTC were positive for BRAF(V600E) mutation in plasma and tumor. However, all 3 patients (100%) had lateral lymph node and lung metastasis. CONCLUSION: These findings suggest that the BRAF(V600E) mutation can be detected using a PNA clamp real-time PCR in the blood of PTC patients with lung metastasis. Future studies are warranted to determine clinical significance of serum BRAF(V600E) mutation in large prospective studies.
Adenocarcinoma, Papillary/*genetics/secondary ; Adult ; Aged ; Carcinoma/*genetics/pathology ; DNA Mutational Analysis ; DNA, Neoplasm/*genetics ; Female ; Humans ; Lung Neoplasms/*genetics ; Lymph Nodes/pathology ; Lymphatic Metastasis ; Male ; Middle Aged ; Mutation ; Neoplasm Invasiveness ; Neoplasm Staging ; *Peptide Nucleic Acids ; Prospective Studies ; Proto-Oncogene Proteins B-raf/*genetics ; Real-Time Polymerase Chain Reaction ; Thyroid Neoplasms/*genetics/pathology

OBJECTIVETo detect K-ras gene mutations in plasma free DNA by peptide nucleic acid clamp PCR assay (PNA-PCR) and nested primer PCR, and to analyze the correlation between K-ras mutations and prognosis in patients with metastatic colorectal cancer (mCRC).

METHODSPeripheral blood was collected and free DNA was extracted from plasma in 106 patients with mCRC. Nested primer PCR and PNA-PCR were used to detect K-ras gene mutation in the plasma free DNA. The patients were divided into three groups by K-ras status: wild-type group (wild-type determined by both methods), low mutation group (mutation by PNA-PCR method, wild-type by nested primer PCR method) and high mutation group (mutation by two methods). The correlation between K-ras mutations and prognosis was analyzed.

RESULTSThe mutation rate of K-ras in tumor tissues of the 106 patients was 40.6%. The Mutation rate of K-ras in plasma free DNA detected by PNA-PCR was 31.1%, significantly higher than that of 15.1% detected by nested primer PCR (P = 0.006). The consistent rate of the K-ras status in plasma free DNA detected by PNA-PCR and that in tumor tissue detected by traditional method was up to 83.0%. The median overall survival (OS) of patients of the wild type, low mutation and high mutation groups was 23.5 months, 17.3 months and 13.9 months, respectively (P = 0.002). The median progression-free survival (PFS) of the K-ras wild-type, low mutation and high mutation groups with first-line chemotherapy was 6.8 months, 6.1 months and 3.2 months, respectively (P = 0.002), and the median OS of them were 23.0 months, 15.5 months and 13.9 months, respectively (P = 0.036). The overall response rate (ORR) was improved in the K-ras wide-type patients who received cetuximab combined with chemotherapy as first-line therapy (75.0% vs. 23.4%, P = 0.058). Cetuximab combined with in second-line therapy chemotherapy led to a significant improvement in disease control rate (DCR) ( 100% vs. 35.7%, P < 0.001) as compared with those of chemotherapy alone. COX regression model showed that K-ras status detected by PNA-PCR, ECOG PS, number of surgery and initially metastatic site were independent factors for prognosis.

CONCLUSIONSPNA-PCR for the detection of K-ras mutation in plasma free DNA can be used to substitute the traditional method for detection of K-ras mutation in tumor tissues. The abundance of K-ras mutation in plasma free DNA is an independent prognostic factor for patients with metastatic colorectal cancer.

Adult ; Aged ; Antibodies, Monoclonal, Humanized ; therapeutic use ; Antineoplastic Combined Chemotherapy Protocols ; therapeutic use ; Cetuximab ; Colorectal Neoplasms ; genetics ; metabolism ; pathology ; DNA ; blood ; Disease-Free Survival ; Female ; Follow-Up Studies ; Genes, ras ; Humans ; Liver Neoplasms ; secondary ; Lung Neoplasms ; secondary ; Male ; Middle Aged ; Mutation ; Peptide Nucleic Acids ; Polymerase Chain Reaction ; Remission Induction ; Retrospective Studies ; Survival Rate ; Young Adult ; ras Proteins ; genetics ; metabolism

The aim of this study was to build a gene chip system with surface plasmon resonance (SPR) technique, for which Gamma-peptide nucleic acid (Gamma-PNA) functioned as a probe, in order to improve sensitivity and its specificity. With the use of self-assembled monolayer (SAM) technology, surface chemistry of two-dimensional structure was used. Gamma-PNA was designed according to the bioinformatics, and was plated on the SPR chip modified by SAM. Subsequently, relevant parameters of the experiment were ensured and optimized. The results showed that the performances of Gamma-PNA probe was little affected by the ion concentration of buffer, and it had a strong light signal in a stable state. As the ion concentration was 0, there were still good hybrid reactions; pH value had less influence upon Gamma-PNA probe, and acid environment of buffer could be better. Gamma-PNA probe combined with sensor technologies achieved made the probe with dispensable labels and real-time detection. It also improved the efficiency of the hybridization and the stability, providing the foundation for clinical application.
Nucleic Acid Hybridization ; Nucleic Acid Probes ; Oligonucleotide Array Sequence Analysis ; methods ; Peptide Nucleic Acids ; genetics ; Sensitivity and Specificity ; Surface Plasmon Resonance

OBJECTIVETo study improvement of detection of paternally herited fetal mutant genes for β-globin in maternal plasma by PNA clamp to seek a noninvasive prenatal diagnostic method for β-thalassemia.

METHODSA total of 38 maternal blood samples were collected at 7 to 20 weeks of gestation, samples in which the father carried CD41-42 mutation and mother carried normal gene or the other point mutation for β-thalassemia were examined. The results of fetal DNA in amniotic fluid, cord blood or peripheral blood of newborns were used as the gold standard for comparison. In the study group, the total cell-free DNA was extracted from maternal plasma using QIAamp DNA Blood Mini Kit. After extraction, the total cell-free DNA was separated by agarose gel (1%) electrophoresis, and the cell-free DNA with a size of 100-300 bp was retrieved from the gel slice. Then, the retrieved DNA-free cell underwent PCR amplified with a PNA clamp. The genotype was confirmed by the conventional method (reverse dot blot hybridization), and the results were compared to gold standard. Simultaneously, two control groups with different PCR procedures were set up. The PCR procedure of control group A was amplified with the extracted total cell-free DNA and PNA clamp, and the PCR procedure of control group B was amplified with the retrieved size-fractionated DNA-free cell without PNA clamp.

RESULTSPlasma samples from 38 pregnant women were detected using PCR products for hybridization, the results were compared with the gold standard. Regarding the 21 samples confirmed by gold standard with fetal genotype 41-42M/N, 19, 8, 12 cases were detected as fetal genotype 41-42M in study group, control group A and control group B respectively, the sensitivity was 90.5% (19/21), 38.1% (8/21) and 57.1% (12/21) respectively;Concerning the 17 samples confirmed by gold standard with fetal normal genotype, the amount of false positive cases were 1, 2 and 1 respectively. The respective specificity was 94.1% (16/17), 94.1% (16/17) and 88.2% (15/17) respectively. The respective accuracies were 92.1% (35/38), 63.2% (24/38) and 71.1% (27/38) respectively. The difference in sensitivity and specificity was pairwise compared by means of McNemar's test. There was significant difference between new study group and control group A or control group B (all P﹤0.05).

CONCLUSIONThe method of detection of paternally inherited fetal mutation genes for β-thalassemia using small size of fetal DNA-free cell in maternal plasma with PNA clamp had several advantages of reliable sensitivity, specificity and accuracy, indicating its potential of clinical practicality.

Adolescent ; Adult ; DNA ; blood ; Female ; Humans ; Inheritance Patterns ; Mutant Proteins ; genetics ; Mutation ; Peptide Nucleic Acids ; Pregnancy ; Prenatal Diagnosis ; Young Adult ; beta-Globins ; genetics ; beta-Thalassemia ; diagnosis ; genetics

BACKGROUND: A peptide nucleic acid (PNA) probe-based real-time PCR (PNAqPCR(TM) TB/NTM detection kit; PANAGENE, Korea) assay has been recently developed for the simultaneous detection of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM) in clinical specimens. The study was aimed at evaluation of the performance of PNA probe-based real-time PCR in respiratory specimens. METHODS: To evaluate potential cross-reactivity, the extracted DNA specimens from Mycobacterium species and non-mycobacterial species were tested using PNA probe-based real-time PCR assay. A total of 531 respiratory specimens (482 sputum specimens and 49 bronchoalveolar washing fluid specimens) were collected from 230 patients in July and August, 2011. All specimens were analyzed for the detection of mycobacteria by direct smear examination, mycobacterial culture, and PNA probe-based real-time PCR assay. RESULTS: In cross-reactivity tests, no false-positive or false-negative results were evident. When the culture method was used as the gold standard test for comparison, PNA probe-based real-time PCR assay for detection of MTBC had a sensitivity and specificity of 96.7% (58/60) and 99.6% (469/471), respectively. Assuming the combination of culture and clinical diagnosis as the standard, the sensitivity and specificity of the new real-time PCR assay for detection of MTBC were 90.6% (58/64) and 99.6% (465/467), respectively. The new real-time PCR for the detection of NTM had a sensitivity and specificity of 69.0% (29/42) and 100% (489/489), respectively. CONCLUSIONS: The new real-time PCR assay may be useful for the detection of MTBC in respiratory specimens and for discrimination of NTM from MTBC.
Bronchoalveolar Lavage Fluid/microbiology ; DNA Probes/chemistry/metabolism ; DNA, Bacterial/*analysis ; Humans ; Molecular Typing/*methods ; Mycobacterium tuberculosis/*genetics/isolation & purification ; Nontuberculous Mycobacteria/*genetics/isolation & purification ; Nucleic Acid Hybridization ; Peptide Nucleic Acids/chemistry/*metabolism ; *Real-Time Polymerase Chain Reaction ; Respiratory System/*microbiology ; Sputum/microbiology

OBJECTIVETo identify the effect of PNA CXCR3 on acute rejection of islet allograft.

METHODSThe mice islet transplant models were used. The mice were divided into three groups including saline group, PNA CXCR3 group and mismatch PNA group. In vitro the proliferation capability of T cell was assessed by proliferative responses. RT-PCR and western blot were used to detect the expression of mRNA and protein. Flow cytometry was applied to determine the expression level of CXCR3 in spleen CD3(+) T cells.

RESULTSCompared with saline [(6.72 +/- 1.48) d] and PNA mismatch-treated recipients [(6.54 +/- 0.86) d], PNA CXCR3-treated recipients demonstrated statistically significant prolongation [(9.70 +/- 1.57) d] in functional allograft survival. The CXCR3 mRNA expression level of PNA CXCR3 group (1.06 +/- 0.07) was significantly down-regulated compared with saline (1.98 +/- 0.22) and PNA mismatch (1.87 +/- 0.10) group at the 7th day after transplant. The date showed that CXCR3 protein and lymphocytes proliferation capability was significantly down-regulated in PNA CXCR3 group compared with saline and PNA mismatch group (P<0.01).

CONCLUSIONSThe present study indicates that PNA CXCR3 can inhibit T cell activating and prolonging the survival time of islet allograft and has a substantial therapeutic effect on inhibiting acute allograft rejection.

Animals ; Blotting, Western ; Diabetes Mellitus, Experimental ; surgery ; Graft Rejection ; genetics ; physiopathology ; Graft Survival ; drug effects ; genetics ; physiology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Oligonucleotides, Antisense ; administration & dosage ; genetics ; Pancreas Transplantation ; methods ; Peptide Nucleic Acids ; administration & dosage ; genetics ; Random Allocation ; Receptors, CXCR3 ; genetics ; metabolism ; physiology ; Reverse Transcriptase Polymerase Chain Reaction ; Signal Transduction ; drug effects ; genetics ; physiology ; Transplantation, Homologous

OBJECTIVESTo construct a novel virus-like particulate peptide-nucleic acid vaccine (VPNV) of human telomerase reverse transcriptase (hTERT), and to study its anti-liver cancer immunity.

METHODSA cationic antigenic peptide was synthesized and purified, and then human granulocyte macrophage colony stimulating factor (hGM-CSF) and TERT gene were cloned into the eukaryotic expression vector pTCAE. The peptide was combined with the nucleic acid vaccine to make a VPNV, which was transfected into eukaryotic cell COS-7. The immunogenicity of hGM-CSF and hTERT were detected using ELISA and Western blot. The efficacy of VPNV for inducing antigen specific CTL response was determined using the lactate dehydrogenase release method.

RESULTSVPNV was verified capable to trigger specific CTL responses and has shown a specific cytolytic activity to liver cancer cell HepG2.

CONCLUSIONA VPNV which can stimulate antigen specific CTL response was successfully constructed. This paves the way for our further investigation of anti-liver cancer immunity in mice.

Animals ; Cancer Vaccines ; immunology ; Cloning, Molecular ; Eukaryotic Cells ; metabolism ; Female ; Granulocyte-Macrophage Colony-Stimulating Factor ; genetics ; immunology ; Liver Neoplasms ; immunology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Peptide Nucleic Acids ; genetics ; immunology ; Telomerase ; genetics ; immunology ; Vaccines, DNA ; immunology

OBJECTIVETo investigate the efficiency of a peptide nucleic acid (PNA) delivery system by using liposome via PNA-DNA hybrids and to test the inhibitive action of antisense PNA on expression of multidrug resistance (MDR) related P-glycoprotein (P-gp) in human neuroblastoma cell line SK-N-SH.

METHODSTwo antisense PNAs were designed targeting at MDR-1 mRNA and then combined with partially complement DNAs respectively. The hybrids were delivered into cells using cationic liposome. The transfection efficiency, expression of P-gp and MDR-1 mRNA, intracellular adarimycin (ADM) were measured by flow cytometry, reverse transcription-polymerase chain reaction (RT-PCR), and high performance liquid chromatography (HPLC).

RESULTSTransfection of PNA increased the cell average fluorescence intensity significantly and the extent of increase was dependent on the concentration of PNA. After being transfected by both PNAs, P-gp expression of SK-N-SH cells decreased significantly and the intracellular ADM level was increased by about 3 times. The level of MDR-1 mRNA expression slightly decreased after transfection, but no statistical significance was observed.

CONCLUSIONSPNA can be delivered into tumor cells in form of PNA-DNA hybrids by cationic liposome. Properly designed antisense PNA can inhibit MDR related P-gp expression of SK-N-SH cells efficiently and specifically.

ATP-Binding Cassette, Sub-Family B, Member 1 ; biosynthesis ; genetics ; Animals ; Drug Resistance, Multiple ; genetics ; Humans ; Nervous System Neoplasms ; metabolism ; Neuroblastoma ; metabolism ; Oligonucleotides, Antisense ; pharmacology ; Peptide Nucleic Acids ; pharmacology ; RNA, Messenger ; biosynthesis ; genetics ; Transfection ; Tumor Cells, Cultured